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- PDB-8v9y: X-ray crystal structure of nanobody JGFN4 -

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Basic information

Entry
Database: PDB / ID: 8v9y
TitleX-ray crystal structure of nanobody JGFN4
ComponentsJGFN4
KeywordsANTITOXIN
Biological speciesCamelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsShi, K. / Moller, N. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01-CA214279 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37-AI064064 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Identification and biophysical characterization of a novel domain-swapped camelid antibody specific for fentanyl.
Authors: Gallant, J.P. / Hicks, D. / Shi, K. / Moeller, N.H. / Hoppe, B. / Lake, E.W. / Baehr, C. / Pravetoni, M. / Aihara, H. / LeBeau, A.M.
History
DepositionDec 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: JGFN4


Theoretical massNumber of molelcules
Total (without water)12,9351
Polymers12,9351
Non-polymers00
Water1,09961
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.243, 26.858, 36.962
Angle α, β, γ (deg.)90.000, 106.990, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

21A-239-

HOH

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Components

#1: Antibody JGFN4


Mass: 12935.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.67 Å3/Da / Density % sol: 26.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: RD22EH53, G4.1 20 w/v polyethylene glycol monomethyl ether 2000, 0.1 M Tris pH8.5, 0.2 M Trimethylamine N-oxide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.76→43.63 Å / Num. obs: 7992 / % possible obs: 91.4 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.035 / Rrim(I) all: 0.07 / Net I/σ(I): 10.4
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.278 / Num. unique obs: 400 / CC1/2: 0.901 / Rpim(I) all: 0.359 / Rrim(I) all: 0.226

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→43.63 Å / SU ML: 0.2295 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 25.1477
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2321 404 5.06 %
Rwork0.191 7584 -
obs0.193 7988 91.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.92 Å2
Refinement stepCycle: LAST / Resolution: 1.76→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms839 0 0 61 900
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033872
X-RAY DIFFRACTIONf_angle_d0.59931185
X-RAY DIFFRACTIONf_chiral_restr0.0448134
X-RAY DIFFRACTIONf_plane_restr0.0041154
X-RAY DIFFRACTIONf_dihedral_angle_d13.2978308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.790.164130.2581208X-RAY DIFFRACTION52.37
1.79-1.820.3112140.197287X-RAY DIFFRACTION69.04
1.82-1.850.2015220.1999302X-RAY DIFFRACTION76.42
1.85-1.890.2554230.208362X-RAY DIFFRACTION87.7
1.89-1.930.2945170.2151374X-RAY DIFFRACTION90.72
1.93-1.980.2679230.1732411X-RAY DIFFRACTION98.86
1.98-2.030.3220.1962389X-RAY DIFFRACTION99.28
2.03-2.080.139190.2075432X-RAY DIFFRACTION99.56
2.08-2.140.2598170.2133413X-RAY DIFFRACTION99.31
2.14-2.210.2689220.1874392X-RAY DIFFRACTION99.76
2.21-2.290.2554290.1998358X-RAY DIFFRACTION85.43
2.29-2.380.2199220.1971403X-RAY DIFFRACTION98.61
2.38-2.490.2521180.2172405X-RAY DIFFRACTION97.92
2.49-2.620.1926160.1957436X-RAY DIFFRACTION100
2.62-2.790.1955240.1881408X-RAY DIFFRACTION100
2.79-30.2352160.2029427X-RAY DIFFRACTION100
3-3.310.2657250.1811412X-RAY DIFFRACTION100
3.31-3.780.2288200.163339X-RAY DIFFRACTION79.07
3.79-4.770.1787220.1633381X-RAY DIFFRACTION89.96
4.8-43.630.2419200.1951445X-RAY DIFFRACTION98.31

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